The Buffalo Reference Genome Assembly

We report on the high quality de novo assembly of the water buffalo genome generated from mix of Illumina and 454 data by MSR-CA assembler by the collaboration between the University of Maryland, USA, USDA-ARS, USA and CASPUR, Italy.  The assembly contains 2.76Gb in scaffolds with N50 contig size of 16kb and N50 scaffold size of 1.4Mb. The data for the genome was a mix of 454 and Illumina sequencing.  The majority of the coverage (70x) was produced by the inexpensive Illumina sequencing technology on HiSeq 2000 and GAIIx genome analyzers.  We also generated 2x genome coverage by 20kb 454 paired end reads.  The sequencing was done at USDA-ARS.

The MSR-CA assembler combines the computational efficiency of the de Bruijn graph approach and the greater repeat resolution ability of the overlap-based assembly strategies.  It is available as open-source code at ftp://ftp.genome.umd.edu/pub/MSR-CA/.  MSR-CA is currently the only assembler natively designed to assemble mixtures of Illumina, 454 and Sanger reads.